Re: [R-sig-Geo] Error creating a standard deviation map from raster stack

Mon, 01 Jul 2013 12:15:53 -0700 

Did the sample code I sent not run on your system?  That's strange.


On my machine:


library(raster)
fn <- system.file("external/test.grd", package="raster")
r <- raster(fn)
r2 <- raster(fn)+runif(ncell(r))
s <- stack(r, r2)
nlayers(s)
m<-mean(s)

std<-calc(s, fun = sd)

fun = function(x)
{ sqrt(var(x))
}
sd <- calc(s, fun)

par(mfrow=c(1,2));plot(sd,main = 'sd'); plot(std, main = 'std')

identical(sd, std)
#[1] TRUE

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C

[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] raster_2.1-37 sp_1.0-9

loaded via a namespace (and not attached):
[1] grid_3.0.1      lattice_0.20-15


On Mon, Jul 1, 2013 at 10:14 AM, Zia Uddin Ahmed <[email protected]> wrote:

>  Thanks you so much it works with following code. Zia****
>
> ** **
>
> fun = function(x)****
>
> { sqrt(var(x))****
>
> }****
>
> sd <- calc(s, fun)****
>
> plot(sd)****
>
> ** **
>
> *From:* Andrew Vitale [mailto:[email protected]]
> *Sent:* Monday, July 01, 2013 12:45 PM
> *To:* Zia Uddin Ahmed
> *Cc:* Roman LuÅ¡trik; [email protected]
>
> *Subject:* Re: [R-sig-Geo] Error creating a standard deviation map from
> raster stack****
>
> ** **
>
> Check out ?calc****
>
> ** **
>
> library(raster)****
>
> fn <- system.file("external/test.grd", package="raster")****
>
> r <- raster(fn)****
>
> r2 <- raster(fn)+runif(ncell(r))****
>
> s <- stack(r, r2)****
>
> nlayers(s)****
>
> m<-mean(s)****
>
> std<-calc(s, fun = sd)****
>
> ** **
>
> ** **
>
> On Mon, Jul 1, 2013 at 9:30 AM, Zia Uddin Ahmed <[email protected]> wrote:*
> ***
>
> In my case, object “s” is a set of 22 geo-tif files.
> Thanks
> zia
>
> From: [email protected] [mailto:[email protected]] On Behalf Of Roman
> Luštrik
> Sent: Monday, July 01, 2013 12:09 PM
> To: Zia Uddin Ahmed
> Cc: [email protected]
> Subject: Re: [R-sig-Geo] Error creating a standard deviation map from
> raster stack****
>
>
> What's the class/structure of object `s`?
>
> Cheers,
> Roman
>
> ****
>
> On Mon, Jul 1, 2013 at 4:38 PM, Zia Uddin Ahmed <[email protected]<mailto:
> [email protected]>> wrote:
> I am trying to calculate standard deviation map from a raster stack. I
> have got following error . Any  suggestion?
> > std<-sd(s)
> Error in as.double(x) :
>   cannot coerce type 'S4' to vector of type 'double'
>
> Thanks
> Zia
>
> fn <- system.file("external/test.grd", package="raster")
> s <- stack(fn, fn)
> r <- raster(fn)
> s <- stack(r, fn)
> nlayers(s)
> m<-mean(s)
> std<-sd(s)
>
> > sessionInfo()
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] gstat_1.0-16  rgdal_0.8-10  raster_2.1-37 sp_1.0-9
>
> loaded via a namespace (and not attached):
> [1] grid_3.0.1       intervals_0.14.0 lattice_0.20-15  spacetime_1.0-4
> [5] xts_0.9-3        zoo_1.7-9
> >
>
> -----Original Message-----****
>
> From: [email protected]<mailto:
> [email protected]> [mailto:[email protected]
> <mailto:[email protected]>] On Behalf Of ASANTOS
> Sent: Sunday, June 23, 2013 4:08 PM****
>
> To: Sarah Goslee; [email protected]<mailto:[email protected]>
> Subject: Re: [R-sig-Geo] Problem with NDVI difference with subset image
>
> Hi Dra. Goslee,
>
>              I work in OS linux and I like very much your lssub function,
> despites your notice. I think that the problems are in linux system,
> because:
>
>  > landc<- stack(c("stackIm1.sample.tif","tackIm2.sample.tif"))
> Error in .local(.Object, ...) :
>    `/home/asantos/Documentos/Sensoriamento remoto percevejo
> bronzeador/Contornos/tackIm2.sample.tif' does not exist in the file system,
> and is not recognised as a supported dataset name.
>
> Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",
>  :
>    Cannot create a RasterLayer object from this file. (file does not exist)
>
>
>               When I try to look the geotiff created
> (stackIm1.sample.tif) there are something wrong, because the pictures
> doesn't open (complete example below).
>
> Thanks for your attention,
>
> Alexandre
>
> require(raster)
> require(sp)
> require(rgdal)
> require(landsat)
> #
> #Create raster
> r <- raster(nc=1000, nr=1000)
> set.seed(20130622)
> stackIm1 <- stack(lapply(1, function(x) setValues(r,
> round(runif(ncell(r))* 255))))## Simulation red band
> stackIm2 <- stack(lapply(1, function(x) setValues(r,
> round(runif(ncell(r))* 255))))## Simulation nir
>
> # define projection system
> r.geo <- CRS("+proj=utm +zone=23 +south +datum=WGS84 +units=m +no_defs")
>  # geographical datum WGS84
> proj4string(stackIm1) <- r.geo
> proj4string(stackIm2) <- r.geo
> #
>
> #Create geotiff
> writeRaster(stackIm1, filename="stackIm1.tif",
> format="GTiff",overwrite=TRUE)
> writeRaster(stackIm2, filename="stackIm2.tif",
> format="GTiff",overwrite=TRUE)
> #
>
> #Subset a geotiff image 50 x 50 pixels
> stackIm1.sample<-lssub("stackIm1.tif", "stackIm1.sample.tif", centerx = 0,
> centery = 0, widthx = 50, widthy = 50)
> stackIm2.sample<-lssub("stackIm1.tif", "sstackIm2.sample.tif", centerx =
> 0, centery = 0, widthx = 50, widthy = 50)
> #
> landc<- stack(c("stackIm1.sample.tif","tackIm2.sample.tif"))
>
>
>
>
>
> Em 23/06/2013 12:59, Sarah Goslee escreveu:
> > Hi,
> >
> > What happens?
> >
> > Do you get an error? Where?
> >
> > What is your sessionInfo()?
> >
> > As it says in the lssub() help, this function was written for a
> > particular purpose, is only known to work on linux, and may not be
> > widely applicable.
> >
> > It's a "use at your own risk" kind of function, and you may well be
> > better off using one of the many other methods available for
> > subsetting raster data, which would save you the whole "export as
> > GeoTIFF, subset, reimport" sequence.
> >
> > Sarah
> >
> > On Sun, Jun 23, 2013 at 11:36 AM, Alexandre Santos****
>
> > <[email protected]<mailto:[email protected]>>
> wrote:
> >> Dear Members,
> >>
> >>
> >> I'm having trouble calculating NDVI difference, first the images
> Geotiff can not view using Ubuntu 4.12 64-bit and therefore can not get to
> the NDVI, follow an example:
> >>
> >> require(raster)
> >> require(sp)
> >> require(rgdal)
> >> require(landsat)
> >> #
> >> #Create raster
> >> r <- raster(nc=1000, nr=1000)
> >> set.seed(20130622)
> >> stackIm1 <- stack(lapply(1, function(x) setValues(r,
> round(runif(ncell(r))* 255))))## Simulation red band
> >> stackIm2 <- stack(lapply(1, function(x) setValues(r,
> round(runif(ncell(r))* 255))))## Simulation nir
> >>
> >> # define projection system
> >> r.geo <- CRS("+proj=utm +zone=23 +south +datum=WGS84 +units=m
> +no_defs")    # geographical datum WGS84
> >> proj4string(stackIm1) <- r.geo
> >> proj4string(stackIm2) <- r.geo
> >> #
> >>
> >> #Create geotiff
> >> writeRaster(stackIm1, filename="stackIm1.tif",
> format="GTiff",overwrite=TRUE)
> >> writeRaster(stackIm2, filename="stackIm2.tif",
> format="GTiff",overwrite=TRUE)
> >> #
> >>
> >> #Subset a geotiff image 50 x 50 pixels
> >> stackIm1.sample<-lssub("stackIm1.tif", "stackIm1.sample.tif", centerx =
> 0, centery = 0, widthx = 50, widthy = 50)
> >> stackIm2.sample<-lssub("stackIm1.tif", "sstackIm2.sample.tif", centerx
> = 0, centery = 0, widthx = 50, widthy = 50)
> >> #
> >>
> >> #Calculate NDVI difference
> >>
> >> multi.espc<-stack(c("stackIm1.sample.tif","stackIm2.sample.tif"))
> >>
> >> band3<-raster(multi.espc,1)
> >> band4<-raster(multi.espc,2)
> >>
> >> ndvi<-(band4-band3)/(band4+band3)
> >>
> >> #
> >>
> >>
> >>
>
> --
> ======================================================================
> Alexandre dos Santos
> Proteção Florestal
> Coordenador do curso Técnico em Florestas
> Vice Coordenador do curso de Engenharia Florestal
> IFMT - Instituto Federal de Educação, Ciência e Tecnologia de Mato Grosso
> Campus Cáceres
> Caixa Postal 244
> Avenida dos Ramires, s/n
> Bairro: Distrito Industrial
> Cáceres - MT                      CEP: 78.200-000
> Fone: (+55) 65 8132-8112 (TIM)   (+55) 65 9686-6970 (VIVO)****
>
>          [email protected]<mailto:
> [email protected]>
>
> _______________________________________________
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> [email protected]<mailto:[email protected]>****
>
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>
> _______________________________________________
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>
> [email protected]<mailto:[email protected]>****
>
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>
>
>
> --
> In God we trust, all others bring data.
>
>         [[alternative HTML version deleted]]****
>
>
> _______________________________________________
> R-sig-Geo mailing list
> [email protected]
> https://stat.ethz.ch/mailman/listinfo/r-sig-geo****
>
>
>
> ****
>
> ** **
>
> -- ****
>
> *Andrew P. Vitale*****
>
> Masters Student****
>
> Department of Geography****
>
> University of Nevada, Reno****
>
> (412) 915-3632****
>
> [email protected]****
>



-- 
*Andrew P. Vitale*
Masters Student
Department of Geography
University of Nevada, Reno
(412) 915-3632
[email protected]

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